Finch, Shaw and Arthur are all at gunpoint, and Control asks about Samaritan's location. Finch insists that Congress shut down the project in 2005, but Control presses on that it exists and asks Arthur. Though he tries hard to fight his brain tumor and remember, Arthur is unable to provide Control with an answer. Control leans over to Shaw, telling her that it was a "thrill" watching her work, before ordering her men to execute Shaw and Finch. Root suddenly bursts in with two guns and opens fire, allowing Shaw to use the distraction to escape and free her two partners. Root is shot by Hersh and she tells the other three how to access the elevator out of the building before Hersh crushes her phone and knocks her out.

Finch, Shaw and Arthur make it out of the building and escape in a car before Hersh can stop them.

1979

In Iowa, Harold is packing for his father, who doesn't remember that his son is taking him to an assisted-care center, The Pines. Harold tells him that he'll take care of him later and glances over at the memory circuit he's created. He tells his father that it's more of a friend than a machine, and that one day it will help and protect his father. Harold's father goes to change, saying that he's going to tell everyone at the Pines that is son is going to "change the world."

Finch drives to a bank and explains to Shaw that even though Samaritan's drives are broken, Control can have someone fix them if she can obtain them. Until then, they have to avoid any enemies. They later arrive at the bank, where Arthur begins to drift away into his college memories, bringing up Nathan Ingram. Arthur is sad to learn that Nathan is dead, but Finch switches the subject, asking if Arthur built backup drives for Samaritan. Shaw figures that Arthur would probably not remember until Arthur surprises them by saying he did in fact build a backup, and that he faked his memory loss to get away with lying to Control. He then says that the backup drives are stored in the vault at the bank.

Root, meanwhile, is placed inside a cell in a secure government facility. She meets Control, who offers to help her escape Reese and Finch in exchange for telling her how to access the Machine. Root continues on with witty retorts, but Control is unimpressed. She pulls out a syringe and injects Root with a tranquilizer.

In Colorado, Reese wakes up in a cell, and tells Fusco that it was stupid of the detective to pick a fight with him, going on to say that he is lucky to still be alive. Fusco ignores the comment and says that the sheriff is keeping the two locked up for now.

Back in New York, Finch, Shaw and Arthur go into the bank and Arthur explains that he put the two drives in a safe deposit box. He stomps his medical alert medallion and takes a key out from inside. The bank manager asks them if they need anything, and Arthur gives her his key, identifying himself as Rudiger Smoot.

Control injects Root with an amphetamine, causing her to forcefully wake up. Control explains how she will continue alternating between tranquilizers and amphetamines until Root can provide her with an answer - an interrogation method one can withstand only for so long until their heart explodes. She then reveals a bag full of syringes. Root simply says that the Machine is beyond Control's reach, but Control still injects her with another tranquilizer.

The bank manager takes Finch and Arthur to the safe deposit vault while Shaw works out that Arthur's bank alias, Rudiger, is the name he gave to the interrogator at the hospital in the radiology room. (“Lethe”) Shaw notices Vigilance members using lasers to disable the cameras, and then spots Peter Collier arriving with a team. Shaw warns Finch about Vigilance, and she notices a SWAT team pulling up. She spots Hersh and realizes that his team is disguised as SWAT. Shaw considers her options, but tells Finch that he and Arthur have to get out of the vault. Collier goes to the vault before Finch can escape with his friend, and he has no choice but to close the vault door. As he slams it shut, Collier fires, hitting the bank manager in the leg before the door can fully close.

In Colorado, Fusco says that they should head home but Reese tells him that he has no home and that all they've been doing is delaying the inevitable by saving Numbers. He figures that Fusco will eventually go back to his crooked ways and nothing has changed. Disgusted, Fusco tells Reese that Carter was better than either one of them, and he isn't giving up even though she's dead. He then calls to the waiting sheriff and the man releases them. As Fusco leaves, Reese tells him to thank Finch for the job, and Fusco says that he hasn't heard from Finch and their friend is probably in danger. However, Fusco pretends to think how Reese would, tautingly telling him that saving Finch would still be "pointless" and that they would simply be "delaying the inevitable." Reese is left thinking.

Finch maintains contact with Shaw via radio and she tells him how to treat the bank manager's wound. She admits that she can't take out Collier and his men because they're the only thing keeping Hersh's team from storming the bank.

Hersh calls Collier on the phone and says that he'll let Collier's team walk away in the next sixty seconds. After that, he'll wipe them out. Collier, however, knows that Hersh will kill him and his men no matter what and promises to obtain the Samaritan drives to "expose the abuses that the government has perpetrated upon them." He hangs up and continues with his operation.

Arthur opens the safe deposit box and removes the two Samaritan drives, as well as a handwritten note dated February 2005. It's in Arthur's handwriting but Arthur doesn't remember why he wrote it.

Root, meanwhile, screams in agony, unable to handle her interrogation for much longer. She finally gives in and reveals to Control that she is in fact the interface and needs a phone to communicate with the Machine. Control takes out a cell phone but then puts it down on a table, and Root tells her that the Machine uses her. Control accepts that she is telling the truth and is surprised to learn that Root considers it a superior force. Figuring that the only way to halt Root's contact with the Machine is to do it physically, Control prepares to perform a Stapedectomy on Root's right ear to remove a bone there, but without anesthesia.

Arthur finally works out that he wrote the note one day before Samaritan was shut down, and realizes that he solved the AI problem that day... and that Samaritan was a true sentient AI.

1980

Harold is working with his computer when it catches power and sets on fire. Harold extinguishes the fire and realizes that he needs more power. He hacks into ARPANET to continue powering his machine.

As Hersh prepares to move inside, Collier calls to give Finch one last chance before he blows the vault open, but Finch hangs up on him. Meanwhile, Arthur looks at the drives and Finch advises him to destroy them before they fall into the wrong hands. He finally reveals to Arthur that he and Nathan built the Machine. Arthur is fascinated, but is still unable to destroy what he views as his child. Finch says that their enemies will use Samaritan to enslave others and asks him if that's what he wants for his child. Convinced, Arthur bids his creation farewell and crushes it.

Shaw informs Finch that she has created a pipe bomb nearby, which will detonate along with Vigilance's bombs and blow open an exit to the sewers. Finch says that it's reckless, but Shaw knows that they're out of options, and tells Finch to take cover with Arthur. Collier blows the vault open, and Finch and Arthur get up. They are found by two Vigilance men, but they are shot down by Shaw, who tells Finch and Arthur to get moving.

Hersh and his men burst into the bank, killing off Collier's men. Shaw holds off gunfire while escorting Finch and Arthur down the stairs, but Collier and his four remaining men hold the two at gunpoint and force Shaw to surrender. Once Arthur tells him that he destroyed the drives, Collier figures that having Arthur will be sufficient. He tells his men to dispose of Shaw and Finch, but two SWAT officers open fire from the stairway. Collier manages to escape with two of his men while the officers reveal that they're Fusco and Reese.

While the team escapes into the sewers, Hersh and his men surround the last Vigilance agent. Hersh demands to know the location of the drives, but the man responds by saying, "the tree of liberty must be replenished by the blood of patriots and tyrants." He reveals a hand grenade and detonates it as Hersh and his men take cover.

Root, now deaf on her right ear, reveals to Control that the Machine had been giving her Morse code messages through the phone Control placed on the table earlier. Root tells Control she knows that Control is scared of her, and that she brought a knife along. Root had managed to pickpocket the knife when Control came close by to perform the surgery. The guards in the room have somehow fallen to the ground, having been "disabled" by the Machine, and Root lunges out of her chair at Control, holding the knife to her head. She asks the Machine what to do with Control, and begins speaking the Machine's mind. Control asks what the Machine wants, and the Machine, speaking through Root, tells Control not to follow it or its agents, and that it's trying to save her. Control asks what the Machine is trying to save her from, but Root simply laughs, asking, "isn't she the best?" Control's fate is left unknown.

The next day, Finch takes Arthur to a private hospital. Arthur says that he's glad Finch built the Machine but admits that his memories are fading. Finch tells him that his memories are still there, just hidden. He then gets a call from Root, who is now posing as a civilian out in the city. Root says that if she and Finch had worked together, then Samaritan's drives wouldn't have fallen into the wrong hands. Finch remembers Arthur destroying the drives, but Root says that the bank manager they were with was an impostor who swapped the drives with fakes, the real one having been murdered prior to their arrival. Finch wonders who the woman is.

Root has Finch put Arthur on the line, and she tells Arthur that The Machine has something to send him on his way. The TV that Arthur is watching brings up footage of Arthur's wife, his best times with her and at MIT with Finch. Both Finch and Arthur are stunned.

1980

Harold goes to see his father and warns him that men will soon come to talk to him, and will claim Harold is a traitor. He assures his father that he isn't, but his father no longer remembers who Harold is. Devastated, Harold sees a bird outside and asks his father what kind of bird it is, expecting him to remember from Finch's childhood. However, his father is unable to identify the bird. Harold hands his father a book about birds, kisses him on the head, and leaves.

Reese goes to the Library to see Finch, who explains how the Machine helped Root escape. He welcomes Reese home, but Reese says that he only came back to protect Finch. Reese no longer trusts the Machine, pointing out that blindly trusting it got Carter killed. He wonders if the Machine cares who matters and who doesn't anymore, and says goodbye. Finch says that he can't go but Reese walks away.

That night, the fake bank manager meets with her employer: Greer. He confirms that she didn't check the contents of the two drives and that she didn't tell anyone about them. Once he's satisfied, Greer shoots her dead to cover his trail. As he walks away, Greer promises Samaritan that it is "destined for great things."